TIMELINE FOR RESEARCH

NOTE - see bottom of page for previous weeks' schedules and things to catch up on.
Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window.

Looking for the Presentation Schedule? - see the Schedule Fall15 ( Semester)

This also has the Presentation Guidelines for all 3 types of presentations: Research Presentations, Technical Presentations, Journal Club Presentations

Link to Research Progress Table
Wikispaces check on every other Sunday (Bi-weekly)
Class slides are uploaded to CANVAS after each class.

This Week	This Week
SPRINGERSWEEK 15 Finish up research for the semester. All ligands should be docked Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library. HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf Final 5 compounds can be uploaded to Screened Compounds spreadsheet on GDocs https://docs.google.com/spreadsheets/d/1pFn32b7cq9xZP8GIjWB1cTieH4xvGFmCJnUNdXt1ecs/edit?usp=sharing If you got to secondary PCR, you should have tried a cloning round. 30-Nov Monday Computer Lab Help session 3-5 1-Dec Tuesday Peer Review of M&M Expr, Pur, Char 2-Dec Wednesday Class A - 2-3 PM Computer Lab Help session 3-5 Class B - 5-6 PM 3-Dec Thursday Lab cleanup -see sheet for items. Then have a mentor sign you off on the line for the things you completed https://drive.google.com/file/d/0B_Gl3lMyhDsoc21pYmJlc3lSbXM/view?usp=sharing Just Added! Computer Lab Help session 2-6 (in the Other computer lab WEL 2.144) 4-Dec Friday Computer Lab Help session 3-6 Lab cleanup -con't 5-Dec Saturday 6-Dec Sunday Final Report due at 9pm Wikispaces due 7-Dec Monday Final Notebook due at 9pm	VETERANSWEEK 15 Finish up research for the semester. All ligands should be docked If you got to secondary PCR, you should have tried a cloning round. Final 5 compounds can be uploaded to Screened Compounds spreadsheet on GDocs https://docs.google.com/spreadsheets/d/1pFn32b7cq9xZP8GIjWB1cTieH4xvGFmCJnUNdXt1ecs/edit?usp=sharing 30-Nov Monday 1-Dec Tuesday Peer Review of M&M Expr, Pur, Char 2-Dec Wednesday Class A - 2-3 PM Class B - 5-6 PM 3-Dec Thursday Lab cleanup -see sheet for items. Then have a mentor sign you off on the line for the things you completed https://drive.google.com/file/d/0B_Gl3lMyhDsoc21pYmJlc3lSbXM/view?usp=sharing 4-Dec Friday Lab cleanup - con't 5-Dec Saturday 6-Dec Sunday Final Report due at 9pm Wikispaces due 7-Dec Monday Final Notebook due at 9pm


Next Week	Next Week

Create/Update Target page on Wikispaces for your Team's target

List of Assignments:
LabNotebooks A, B, C, D, ....
Wikispaces (Bi-Weekly)
Safety
Target Page
LICpNIC-Bsa4cloningExercise
Misc mini-assignments or quizzes
Journal Club presentation and Question sheets
Technical Presentation (if applicable)
Research Presentation
PyMol Refresher
Virtual Screening Refresher
Mid-Semester Research Report on Target
Draft of M&M Cloning
Draft of M&M Virtual
Draft of M&M Express,Pur,Char
Final Report

2 Weeks Blocks layout

In general your progress will be assessed every 2 weeks (lab hours, research progress, wikispaces updates)
26-Aug Wednesday - 6-Sep Sunday (1.5 wks)
7-Sep Monday - 20-SepSunday
21-SepMonday - 4-Oct Sunday
5-Oct Monday - 18-OctSunday
19-OctMonday - 1-Nov Sunday
2-Nov Monday - 15-Nov Sunday
16-Nov Monday - 29-Nov Sunday
30-Nov Monday - 6-Dec Sunday

RECURRING ITEMS:
Wikispaces posting due - Sundays at 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the captions to let the reader (Dr. B) understand what it is.

Lab Notebook check - Saturdays at 5pm

REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.

DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
Info from your Target Page (which means you need a Target page first!)

Update Target page on Wikispaces (need all the info from the list of items)
- if you don't have a Target page - start making it for your Target .

ITEMS FOR LATER:
Cut pNIC-Bsa4 that you grew up with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check

Tail Primer Design and Ordering

Make LB+Kan plates (4) -
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)

Make LB + Kan/Suc plates (6)
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)

mmmmm

After Fire Safety Training is uploaded:
PAPER COPY – Print out of TxClass Safety Training -
- (can put in Safety section of VDS sign-in binder in lab)

Project Tasks (in rough order):
Nanodrop & Submit to DNA Sequencing (1.5 hrs)
Target Selection Form

Dilute some primers from lyophilized powder: random ones (pLIC-for & pLIC-rev)?
-- make working dilution in water from 100uM stock.
-- Store working dilution in YOUR own box.

Make 500ml of LB and autoclave (with mentor)
Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones)
---- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5

Midi-prep (in pairs) -
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Submit to DNA Sequencing for YOUR pNIC-Bsa4 that you grew up

Analyze DNA Sequence Exercise (as a group)

Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall15.doc - 2 hrs

upload final primers to Google Docs/VDS/Misc/Primers/PrimerPlateOrderFall2015
post final primers to Wikispaces Target page

'My Second PCR' - PCR pLIC using pNIC-Bsa4
Set up target protein for Virtual Screening

Design Tail Primers for targets, order tail primers
Primer Dilution for your own primers

Create or Revise your Target page (not same as your Research Page)
LICpNIC-Bsa4cloningExerciseVDS_Fall15

Make Oligo mix for Targets

Expression
Purification
Characterization
PROTEIN INFO
Enter your protein yields into: Protein Spectrophotometer Calc
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodC1mRVpNLVlDOUE4NlNxdldqNEZwRmc&usp=sharing

Virtual Work
screening Due ?

M&M's
Cloning Materials & Methods due @ ???
-- see guidelines on GDocs

Peer Review of M&M Cloning is due @ ???
- you will have 2 to review
- make 5 constructive criticisms
- make 2 compliments

Virtual M&M due @ ???
Expression, Purification, Characterization M&M due @ ???
-- see guidelines on GDocs

Peer Review due ??:
M&M Virtual

Peer Review due ??:
M&M Expression, Pur, Char

Finish virtual screening
Enzyme Assay protocol
Inhibition Assay protocol

Graded Assignments:
HOURS:
Week1&2 Hrs
Week 3&4 Hrs
......

2015 Dates:

Week1 Yes - you do need lab hours for week 1 (just 4 hrs - so, get in lab and review your notebook & plan) 26-Aug Wednesday 27-Aug Thursday sign up for Fire Safety training (see link to left 'Required Lab Safety') Lab times open for Nanodrop and Submit to DNA sequencing See Submit to DNA Sequencing protocol (in GDrive/Protocols) for Instructions: Link to create dnaLIMS Account: (must make an account before submitting DNA to sequencing) http://146.6.133.14/cgi-bin/dna/loginNn.cgi* --- sign up on sheet above Print protocols as '2 sheets per page' Nanodrop protocol Submit to DNA Sequencing Create your Research Page on Wikispaces and post your first results - see page for Instructions 28-Aug Friday 29-Aug Saturday 30-Aug Sunday	Week1 Yes - you do need lab hours for week 1 (just 3-4 hrs - so, get in lab and review your notebook & plan) 26-Aug Wednesday 27-Aug Thursday planning startup your cloning work again 28-Aug Friday planning startup your cloning work again 29-Aug Saturday 30-Aug Sunday
WEEK 2 Be sure you have 8-10hrs/week - for the 1st week of class that should be about 2-3 hrs since the lab was only open for 2 days See Week1 items at bottom of page for things that you didn't get to. Items for This Week sign up for Fire Safety training (see link to left 'Required Lab Safety') Create your own folder in Google Docs under the folder: /StudentFolders create your Research Page on Wikispaces Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) - sign up for specific times -- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5.doc Make 500ml of LB and autoclave (with mentor) - anytime mentor available Dilute some primers (if they come in) - anytime mentor available RE Digest - at specific times For protocols, look in GDrive/VDSClass/Protocols/FirstProtocols 31-Aug Monday Transformation times (must start on time) Make 500ml of LB and autoclave (with mentor) 1-Sep Tuesday Transformation times (must start on time) Make 500ml of LB and autoclave (with mentor) 2-Sep Wednesday Class A - 2-3 PM Location: see the Schedule Fall 15 (Semesterly) Class B - 5-6 PM Location: GEA 125 Make 500ml of LB and autoclave (with mentor) Dilute some primers (if they come in) Transformation times at 5:30 PM (must start on time) 3-Sep Thursday RE Digest 4-Sep Friday RE Digest 5-Sep Saturday Lab Notebook @ 5pm - lab will be open for notebooks - no mentors on staff yet. So, if you need the lockbox code - email Andee or one of the mentors. Springers should not be doing lab work on Saturdays. Only Veterans can do Saturday work right now. 6-Sep Sunday Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015	WEEK 2 Get some hours in lab PyMol refresher exercise - see/GDrive/Protocols/VirtualProtocols 31-Aug Monday 1-Sep Tuesday 2-Sep Wednesday Class A - 2-3 PM Location: see the Schedule Fall 15 (Semesterly) Class B - 5-6 PM Location: GEA 125 3-Sep Thursday 4-Sep Friday 5-Sep Saturday - no mentors on staff yet. So, if you need the lockbox code - email Andee or one of the mentors. Springers should not be doing lab work on Saturdays. Only Veterans can do Saturday work right now and must be with another equally trained VDSer. 6-Sep Sunday Wikispaces posting due - 9 pm
WEEK 3 Items for This Week RE Digest gel check Analyze DNA Sequence -in comp lab Grow up 160 ml of pNIC-Bsa5 and save for later. 7-Sep Monday - Labor Day - No Lab 8-Sep Tuesday 4-6:30 pm - Analyze DNA Sequence Exercise (as a group) - in WEL 2.144 Comp Lab 9-Sep Wednesday Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125 Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet): 4, 5 or 6 PM (takes 1 hour) - start overnight cultures of plasmids in DH5alpha for midi prepping later. -Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan --pNIC-Bsa4 is a 'low copy' plasmid --spin down next morning (10-11 am) - make sure a mentor can be there! (save in -20degC or proceed to Midi-Prep - 2-3hrs) -- if you don't' have time to spin down in morning (~30-45 min), you can temporarily store your growth flask in 4degC for a few hours til you can spin it in the afternoon. Pellets can be frozen and stored til next day or so. In order to make lots of plasmid that we will need for cloning: -- Plasmid Midi-prep (in pairs) - use Tony's new protocol 10-SepThursday come in to lab in morning to spin down overnight cultures 3:30 -6:30 pm - Analyze DNA Sequence Exercise (as a group) - in WEL 2.144 Comp Lab Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet): 4, 5 or 6 PM (takes 1 hour) ProtocolPCRVDS.xls - 11-SepFriday come in to lab in morning to spin down overnight cultures Analyze RE digest on a gel ProtocolPCRVDS.xls 12-SepSaturday 13-SepSunday	WEEK 3 Virtual Work PyMol Refresher: Virtual Volunteers from summer don’t have to do this! (Kevin H, Bethany, Jeff, Lisa, Steven, Diane) can count as 2 hours of lab time start Virtual Screening Refresher - see GDocs/Protocols/VirtualProtocols 7-Sep Monday - Labor Day - No Lab 8-Sep Tuesday 4-6:30 pm - PyMol & Virtual Screening help in WEL 2.144 Comp Lab 9-Sep Wednesday Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125 10-SepThursday 4-6:30 pm - Virtual Screening help in WEL 2.144 Comp Lab PyMol Refresher - due 11-SepFriday Create/Update Target page on Wikispaces for your Team's target 12-SepSaturday 13-SepSunday
WEEK 4 Items for This Week 'My First PCR' - using pGBR22 (repeat until it works) - ProtocolPCRVDS.xls Run gel to check it Target Selection Form - once Dr. B sends the link PyMol Refresher MidiPrep of your pNIC-Bsa4 that you grew up last week Second Practice PCR (pLIC primers on pNIC-Bsa4): ProtocolPCR_pLICsequencing15.xl Maybe: Oligo Primer Design Tail Primer Design and Ordering 14-SepMonday 15-SepTuesday 1st Mini Meetings - All Groups 16-SepWednesday Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125 17-SepThursday 18-SepFriday 19-SepSaturday 20-SepSunday Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015	WEEK 4 Create/Update Target pages Wet Lab continue cloning, expression, purification, storage look up your substrates and how to order them look up enzyme assay in other research papers Virtual Work start Virtual Screening Refresher - see GDocs/Protocols/VirtualProtocols Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall14.doc 14-SepMonday 15-SepTuesday Virtual Refresher Help Session ? 1st Mini Meetings - All Groups 16-SepWednesday Class A - 2-3 PM Location: PAI 5.33 Virtual Refresher Help Session? Class B - 5-6 PM Location: GEA 125 17-SepThursday Virtual Refresher Help Session Virtual Screening Refresher due 18-SepFriday 19-SepSaturday 20-SepSunday Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015
WEEK 5 Items for This Week Repeat - 'My First PCR' - if failed Second Practice PCR (pLIC primers on pNIC-Bsa4): ProtocolPCR_pLICsequencing15.xl Oligo Primer Design Tail Primer Design and Ordering PyMol Refresher Make Oligo Mix for your targets (each person makes own) ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx Scheduled Times for Lab https://docs.google.com/spreadsheets/d/1QK6fn8avAAYZ6SJb8GStMUCcPc1zKRMzpUrXuQhegqQ/edit?usp=sharing 21-SepMonday Oligo Primer Design & Ordering for Targets 22-SepTuesday Oligo Primer Design & Ordering for Targets 23-SepWednesday Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125 24-SepThursday 6-7:30 PyMol Refresher Help session in WEL 2.128 can count as 2 hours of lab time 25-SepFriday 3-5:30 PyMol Refresher Help session in WEL 2.128 can count as 2 hours of lab time 26-SepSaturday PyMol Refresher - due for springers Lab Notebook @ 5pm - lab will be open for notebooks What Goes Where for notebook?: PyMol Refresher Analyze DNA Sequence RE Digest PCR & run on an agarose gel (if done) Oligo Design - protocol and DNA Works output file Tail Primer Design - protocol and results of what you are ordering 27-SepSunday Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15	WEEK 5 21-SepMonday 22-SepTuesday 23-SepWednesday Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125 24-SepThursday 25-SepFriday 26-SepSaturday Lab Notebook @ 5pm - lab will be open for notebooks 27-SepSunday Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15 .doc
WEEK 6 Items for This Week Second Practice PCR (pLIC primers on pNIC-Bsa4): - on your own - ProtocolPCR_pLICsequencing15.xl Make Oligo Mix for your targets each person makes own ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx Primary PCR ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx Schedule for this week: 28-SepMonday 29-SepTuesday Mini Meetings for ALL this time 2pm - Bacteria 2:30 pm - Fungi 5pm - Protozoa 5:30 pm - Viruses 30-SepWednesday Class A - 2-3 PM Class B - 5-6 PM 1-Oct Thursday 2-Oct Friday Virtual Screening Refresher - start looking at will be due next week 3-Oct Saturday 4-Oct Sunday Mid Semester Research Report Due GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15	WEEK 6 Items for This Week Control ligands should be selected (Pos & Neg) LigPrep your control ligands Select your protein structure, run Molprobity on it, Upload to DDFE Determine active site and which substrates/metals should or should not be in place Dock control ligands VS Help Session times with Dr. B - Mon - Tues ? - Wed, - Thurs - Fri 28-SepMonday 29-SepTuesday Mini Meetings for ALL this time 2pm - Bacteria 2:30 pm - Fungi 5pm - Protozoa 5:30 pm - Viruses 30-SepWednesday Class A - 2-3 PM 3-5: VS Help Session - in 'main' Comp Lab (WEL 2.128) Class B - 5-6 PM 1-Oct Thursday VS Help Session - in 'other' Comp Lab (WEL 2.144) 2-Oct Friday 3-Oct Saturday 4-Oct Sunday Mid Semester Research Report Due GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15
WEEK 7 Items for the Week Finish practice PCRs you must have a working practice PCR (either pGBR22 or pNIC pcr. If you aren't sure - let Dr. B check it on your Research Page) Virtual Screening Refresher (worth 2hrs of lab time) Primary PCR Primer Dilution of your own tail primers (you've done a primer dilution before) Secondary PCR Wet lab will be Open Times this week - just come in whenever a mentor is present. Shoot for 8-10 hrs at least for the week while moving your project forward. 5-Oct Monday 2:30 - 6pm WEL 2.128 Help Session - VS Refresher & Mid Semester Res Report 3-6 Mentors on staff in wet lab 6-Oct Tuesday no mini-meetings 4 - 6:30 pm WEL 2.144 Help Session - VS Refresher & Mid Semester Res Report 3-6 Mentors on staff in wet lab 7-Oct Wednesday Class A - 2-3 PM 3-5pm WEL 2.128 Help Session - VS Refresher & Mid Semester Res Report 3-6 Mentors on staff in wet lab Class B - 5-6 PM 8-Oct Thursday 3:30 - 6:30 pm WEL 2.144 Help Session - VS Refresher & Mid Semester Res Report 3:30 -7 Mentors on staff in wet lab 9-Oct Friday 2:30 - 4:30 pm WEL 2.128 Help Session - VS Refresher 2-6:30 Mentors on staff in wet lab 10-OctSaturday 11-OctSunday	WEEK 7 Items for the Week finish Control Ligs docking (discuss with Dr.B) start docking of a medium library (e.g. CB306 and Maybridge HF9) HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf finish cloning ....... See the Springers side for the Virtual Help sessions 5-Oct Monday 6-Oct Tuesday no mini meetings 7-Oct Wednesday Class A - 2-3 PM Class B - 5-6 PM 8-Oct Thursday 9-Oct Friday 10-OctSaturday 11-OctSunday
WEEK 8 Items for the Week Tail Primer dilution Secondary PCR PCR squared Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands 12-OctMonday 4:30- 6:30 pm WEL 2.128 (or maybe WEL 2.144) Help Session - VS Refresher Open Labs: 3:30-7 13-OctTuesday Mini Meetings for some Open Labs: 3:00 -7 14-OctWednesday Class A - 2-3 PM Open Labs: 3:00-7 Class B - 5-6 PM 15-OctThursday Open Labs: 3:00-7 16-OctFriday Open Labs: 2-7 17-OctSaturday Lab Notebook due 18-OctSunday Target Page due for Springers (see Target pages on Wikispaces) Peer Review of Mid Semester Research Report due	WEEK 8 Items for the Week finish docking of a medium library HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf Start docking of Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf finish cloning ....... 12-OctMonday 13-OctTuesday Mini Meetings for some 14-OctWednesday Class A - 2-3 PM Class B - 5-6 PM 15-OctThursday 16-OctFriday 17-OctSaturday 18-OctSunday
WEEK 9 Items for the Week Secondary PCR PCR squared Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands Start cloning rounds Pick control ligands for VS 19-OctMonday 20-OctTuesday Mini Meetings for some 21-OctWednesday Class A - 2-3 PM Class B - 5-6 PM 22-OctThursday 23-OctFriday 24-OctSaturday Lab Notebook due pNIC-Bsa4 exercise do (on paper) - put in your notebook as loose leaf 25-OctSunday M&M Cloning due - see Canvas for link	WEEK 9 Items for the Week continue docking of Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf start protein expression trial 19-OctMonday 20-OctTuesday Mini Meetings for some 21-OctWednesday Class A - 2-3 PM Class B - 5-6 PM 22-OctThursday 23-OctFriday 24-OctSaturday Lab Notebook due pNIC-Bsa4 exercise do (on paper) - put in your notebook as loose leaf 25-OctSunday M&M Cloning due - see Canvas for link
WEEK 10 Items for the Week PCR squared Pick control ligands for VS (see computer lab times for help) Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands Start cloning rounds Dock control ligands for VS Control Ligands Instructions: Make folder for target in /Projects Folder in VDS Class. Create a Google Spreadsheet for your control ligands (WITHIN the shared folder), and split the positive and negative ligands between each member. Split the positive ligands evenly amongst the group and then each person should do at least 2 negative control ligands. Then place copies of your downloaded ligands into the folder When you start your Lig Prep for virtual screening – upload the ligands files into your own folder on the DDFE Wet Lab: check the calendar for when mentors will be on to help 26-OctMonday Comp lab help: 3-5 pm 27-OctTuesday Mini Meetings for some 28-OctWednesday Class A - 2-3 PM Comp lab help: 3-5 pm Class B - 5-6 PM 29-OctThursday 30-OctFriday Comp lab help: 3-5 pm 31-OctSaturday Finish picking control ligands 1-Nov Sunday Peer Review of M&M Cloning Due Wikispaces due Weeks 8,9,10	WEEK 10 Items for the Week finish docking of Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf express protein purify protein enzyme assay test 26-OctMonday 27-OctTuesday Mini Meetings for some 28-OctWednesday Class A - 2-3 PM Class B - 5-6 PM 29-OctThursday 30-OctFriday 31-OctSaturday 1-Nov Sunday Peer Review of M&M Cloning Due Wikispaces due Weeks 8,9,10
WEEK 11 Items for the Week PCRs Dock control ligands for VS (see computer lab times for help) Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands Start cloning rounds Dock control ligands for VS Wet Lab: check the calendar for when mentors will be on to help 2-Nov Monday Start to dock control ligs 3-5 pm computer lab help session WEL 2.128 3-Nov Tuesday Mini Meetings for some 4-Nov Wednesday Class A - 2-3 PM 3-5 pm computer lab help session WEL 2.128 Class B - 5-6 PM 5-Nov Thursday 6-Nov Friday 3-5 pm computer lab help session WEL 2.128 7-Nov Saturday Finish docking control ligs 8-Nov Sunday M&M Virtual due	WEEK 11 Items for the Week analyze results of Screening 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf finish cloning express protein purify protein enzyme assay test 2-Nov Monday 3-Nov Tuesday Mini Meetings for some 4-Nov Wednesday Class A - 2-3 PM Class B - 5-6 PM 5-Nov Thursday 6-Nov Friday 7-Nov Saturday 8-Nov Sunday M&M Virtual due
WEEK 12 9-Nov Monday Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands Start cloning rounds start docking of medium libraries HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf 10-Nov Tuesday Mini Meetings for some 11-Nov Wednesday Class A - 2-3 PM 3- 5- Computer Lab help session WEL 2.128 Class B - 5-6 PM 12-Nov Thursday 13-Nov Friday 3- 5- Computer Lab help session WEL 2.128 14-Nov Saturday Lab Notebook Due 15-Nov Sunday 24th -NOV finish docking of a medium libraries HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf	WEEK 12 Items for the Week upload top 5 compunds to ScreenedCompounds spreadsheet in GDrive finish cloning express protein purify protein enzyme assay test... 9-Nov Monday 10-Nov Tuesday Mini Meetings for some 11-Nov Wednesday Class A - 2-3 PM Class B - 5-6 PM 12-Nov Thursday 13-Nov Friday 14-Nov Saturday Lab Notebook Due 15-Nov Sunday
WEEK 13 Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol) gel check it to confirm 2 bands Start cloning rounds Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library. HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf Wet Lab: check the calendar for when mentors will be on to help 16-Nov Monday 4 - 5:30- Computer Lab help session WEL 2.128 17-Nov Tuesday Mini Meetings for some 18-Nov Wednesday Class A - 2-3 PM 3- 5- Computer Lab help session WEL 2.128 Class B - 5-6 PM 19-Nov Thursday Just Added ! 2-6- Computer Lab help session WEL 2.144 (the other comp lab) 20-Nov Friday 3- 5- Computer Lab help session WEL 2.128 21-Nov Saturday 22-Nov Sunday	WEEK 13 Items for the Week upload top 5 compounds to ScreenedCompounds spreadsheet in GDrive finish cloning express protein purify protein enzyme assay test... 16-Nov Monday 17-Nov Tuesday Mini Meetings for some 18-Nov Wednesday Class A - 2-3 PM Class B - 5-6 PM 19-Nov Thursday 20-Nov Friday 21-Nov Saturday 22-Nov Sunday
WEEK 14 continue cloning - if your Secondary PCR works - you should attempts a cloning roung. Virtual Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library. HF9PlatesPlates5_9.sdf cb_306_3d.sdf LOPAC_3d.sdf NIH_ClinCol3Ded.sdf 23-Nov Monday Computer Lab Help session 3-6 Wet lab open 24-Nov Tuesday Wet lab open 25-Nov Wednesday No Class wet lab open 26-Nov Thursday - THANKSGIVING 27-Nov Friday 28-Nov Saturday 29-Nov Sunday	WEEK 14 finish virtual finish cloning test your enzyme 23-Nov Monday 24-Nov Tuesday 25-Nov Wednesday No Class 26-Nov Thursday - THANKSGIVING 27-Nov Friday 28-Nov Saturday 29-Nov Sunday

Timeline F15

TIMELINE FOR RESEARCH

This Week

This Week

Next Week

Next Week

2 Weeks Blocks layout

Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):

Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):